[gmx-users] pme problems in gromacs 3.3
David L. Bostick
dbostick at physics.unc.edu
Fri Nov 11 23:11:23 CET 2005
If I recall correctly, Erik fixed this bug and put a copy of pme.c that
should replace the 3.3 distribution pme.c on the gromacs ftp site. One
can check the user archives to see the directory. The fix should allow a
larger pme spline order.
David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
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On Fri, 11 Nov 2005, David wrote:
> On Fri, 2005-11-11 at 14:53 -0500, hseara at netscape.net wrote:
> > Thanks David,
> >
> > Now everything seems to work. But why with order 6 was working in
> > 3.2.1 and not now? can you give me a reference where I can learn more
> > about what all pme parameter mean? and how to set up them?.
>
> Documentation in the papers.
>
> I seem to recall that a bug was introduced for pme_order != 4 in the 3.3
> release, that was fixed recently. What is the problem you are seeing?
> Maybe you can file a bugzilla for this and upload a 3.2.1 tpr file that
> reproduces the problem.
>
>
>
> >
> > Thank you, Hector
> >
> > -----Original Message-----
> > From: David <spoel at xray.bmc.uu.se>
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Sent: Fri, 11 Nov 2005 20:21:50 +0100
> > Subject: Re: [gmx-users] pme problems in gromacs 3.3
> >
> > On Fri, 2005-11-11 at 14:07 -0500, hseara at netscape.net wrote:
> > > Dear everyone,
> > >
> > > I'm trying to perform a bilayer simulation with the new gromacs 3.3
> > > that works fine with the older version 3.2.1. The problem as far as I
> > > know is related to something around "pme". When I turn it off and use
> > > cut-off every think works fine. Here is my dun.mdp file when I turn pme
> > > on in gromacs 3.3. The same system in gromacs 3.2.1 with this pme file
> > > works perfectly. Any help will be apreciated.
> >
> >
> > try pme_order = 4
> >
> >
> > >
> > > ;
> > > ; File 'mdout.mdp' was generated
> > > ; By user: hector (500)
> > > ; On host: hectorp
> > > ; At date: Tue Nov 8 22:26:19 2005
> > > ;
> > >
> > > ; VARIOUS PREPROCESSING OPTIONS
> > > title = MD run on DOPS
> > > ; Preprocessor - specify a full path if necessary.
> > > cpp = /usr/bin/cpp
> > > include =
> > > define =
> > >
> > > ; RUN CONTROL PARAMETERS
> > > integrator = md
> > > ; Start time and timestep in ps
> > > tinit = 0
> > > dt = 0.001
> > > nsteps = 20000
> > > ; For exact run continuation or redoing part of a run
> > > init_step = 0
> > > ; mode for center of mass motion removal
> > > comm-mode = Linear
> > > ; number of steps for center of mass motion removal
> > > nstcomm = 1
> > > ; group(s) for center of mass motion removal
> > > comm-grps =
> > >
> > > ; LANGEVIN DYNAMICS OPTIONS
> > > ; Friction coefficient (amu/ps) and random seed
> > > bd-fric = 0
> > > ld-seed = 1993
> > >
> > > ; ENERGY MINIMIZATION OPTIONS
> > > ; Force tolerance and initial step-size
> > > emtol = 50
> > > emstep = 0.05
> > > ; Max number of iterations in relax_shells
> > > niter = 0
> > > ; Step size (ps^2) for minimization of flexible constraints
> > > fcstep = 0
> > > ; Frequency of steepest descents steps when doing CG
> > > nstcgsteep = 15000
> > > nbfgscorr = 10
> > >
> > > ; OUTPUT CONTROL OPTIONS
> > > ; Output frequency for coords (x), velocities (v) and forces (f)
> > > nstxout = 500
> > > nstvout = 500
> > > nstfout = 0
> > > ; Checkpointing helps you continue after crashes
> > > nstcheckpoint = 1000
> > > ; Output frequency for energies to log file and energy file
> > > nstlog = 500
> > > nstenergy = 500
> > > ; Output frequency and precision for xtc file
> > > nstxtcout = 0
> > > xtc-precision = 1000
> > > ; This selects the subset of atoms for the xtc file. You can
> > > ; select multiple groups. By default all atoms will be written.
> > > xtc-grps =
> > > ; Selection of energy groups
> > > energygrps =
> > >
> > > ; NEIGHBORSEARCHING PARAMETERS
> > > ; nblist update frequency
> > > nstlist = 3
> > > ; ns algorithm (simple or grid)
> > > ns_type = grid
> > > ; Periodic boundary conditions: xyz (default), no (vacuum)
> > > ; or full (infinite systems only)
> > > pbc = xyz
> > > ; nblist cut-off
> > > rlist = 0.95
> > > domain-decomposition = no
> > >
> > > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > > ; Method for doing electrostatics
> > > coulombtype = pme
> > > rcoulomb-switch = 0
> > > rcoulomb = 0.95
> > > ; Relative dielectric constant for the medium and the reaction field
> > > epsilon-r = 1
> > > epsilon_rf = 1
> > > ; Method for doing Van der Waals
> > > vdw-type = Cut-off
> > > ; cut-off lengths
> > > rvdw-switch = 0
> > > rvdw = 1.8
> > > ; Apply long range dispersion corrections for Energy and Pressure
> > > DispCorr = EnerPres
> > > ; Extension of the potential lookup tables beyond the cut-off
> > > table-extension = 1
> > > ; Seperate tables between energy group pairs
> > > energygrp_table =
> > > ; Spacing for the PME/PPPM FFT grid
> > > fourierspacing = 0.12
> > > ; FFT grid size, when a value is 0 fourierspacing will be used
> > > fourier_nx = 0
> > > fourier_ny = 0
> > > fourier_nz = 0
> > > ; EWALD/PME/PPPM parameters
> > > pme_order = 6
> > > ewald_rtol = 1e-05
> > > ewald_geometry = 3d
> > > epsilon_surface = 0
> > > optimize_fft = no
> > >
> > > ; GENERALIZED BORN ELECTROSTATICS
> > > ; Algorithm for calculating Born radii
> > > gb_algorithm = Still
> > > ; Frequency of calculating the Born radii inside rlist
> > > nstgbradii = 1
> > > ; Cutoff for Born radii calculation; the contribution from atoms
> > > ; between rlist and rgbradii is updated every nstlist steps
> > > rgbradii = 2
> > > ; Salt concentration in M for Generalized Born models
> > > gb_saltconc = 0
> > >
> > > ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
> > > implicit_solvent = No
> > >
> > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> > > ; Temperature coupling
> > > Tcoupl = nose-hoover
> > > ; Groups to couple separately
> > > tc-grps = DOPS DOPA SOL NA+
> > > ; Time constant (ps) and reference temperature (K)
> > > tau-t = 0.2 0.2 0.2 0.2
> > > ref-t = 303.0 303.0 303.0 303.0
> > > ; Pressure coupling
> > > Pcoupl = Parrinello-Rahman
> > > Pcoupltype = semiisotropic
> > > ; Time constant (ps), compressibility (1/bar) and reference P (bar)
> > > tau_p = 1.0 1.0
> > > compressibility = 4.5e-5 4.5e-5
> > > ref_p = 1.01325 1.01325
> > > ; Random seed for Andersen thermostat
> > > andersen_seed = 815131
> > >
> > > ; OPTIONS FOR QMMM calculations
> > > QMMM = no
> > > ; Groups treated Quantum Mechanically
> > > QMMM-grps =
> > > ; QM method
> > > QMmethod =
> > > ; QMMM scheme
> > > QMMMscheme = normal
> > > ; QM basisset
> > > QMbasis =
> > > ; QM charge
> > > QMcharge =
> > > ; QM multiplicity
> > > QMmult =
> > > ; Surface Hopping
> > > SH =
> > > ; CAS space options
> > > CASorbitals =
> > > CASelectrons =
> > > SAon =
> > > SAoff =
> > > SAsteps =
> > > ; Scale factor for MM charges
> > > MMChargeScaleFactor = 1
> > > ; Optimization of QM subsystem
> > > bOPT =
> > > bTS =
> > >
> > > ; SIMULATED ANNEALING
> > > ; Type of annealing for each temperature group (no/single/periodic)
> > > annealing = no
> > > ; Number of time points to use for specifying annealing in each group
> > > annealing_npoints =
> > > ; List of times at the annealing points for each group
> > > annealing_time =
> > > ; Temp. at each annealing point, for each group.
> > > annealing_temp =
> > >
> > > ; GENERATE VELOCITIES FOR STARTUP RUN
> > > gen_vel = no
> > > gen-temp = 300
> > > gen-seed = 533671
> > >
> > > ; OPTIONS FOR BONDS
> > > constraints = all-bonds
> > > ; Type of constraint algorithm
> > > constraint-algorithm = LINCS
> > > ; Do not constrain the start configuration
> > > unconstrained-start = yes
> > > ; Use successive overrelaxation to reduce the number of shake iterations
> > > Shake-SOR = no
> > > ; Relative tolerance of shake
> > > shake-tol = 0.0001
> > > ; Highest order in the expansion of the constraint coupling matrix
> > > lincs-order = 4
> > > ; Number of iterations in the final step of LINCS. 1 is fine for
> > > ; normal simulations, but use 2 to conserve energy in NVE runs.
> > > ; For energy minimization with constraints it should be 4 to 8.
> > > lincs-iter = 1
> > > ; Lincs will write a warning to the stderr if in one step a bond
> > > ; rotates over more degrees than
> > > lincs-warnangle = 90
> > > ; Convert harmonic bonds to morse potentials
> > > morse = no
> > >
> > > ; ENERGY GROUP EXCLUSIONS
> > > ; Pairs of energy groups for which all non-bonded interactions are
> > > excluded
> > > energygrp_excl =
> > >
> > > ; NMR refinement stuff
> > > ; Distance restraints type: No, Simple or Ensemble
> > > disre = No
> > > ; Force weighting of pairs in one distance restraint: Conservative or
> > > Equal
> > > disre-weighting = Conservative
> > > ; Use sqrt of the time averaged times the instantaneous violation
> > > disre-mixed = no
> > > disre-fc = 1000
> > > disre-tau = 0
> > > ; Output frequency for pair distances to energy file
> > > nstdisreout = 100
> > > ; Orientation restraints: No or Yes
> > > orire = no
> > > ; Orientation restraints force constant and tau for time averaging
> > > orire-fc = 0
> > > orire-tau = 0
> > > orire-fitgrp =
> > > ; Output frequency for trace(SD) and S to energy file
> > > nstorireout = 100
> > > ; Dihedral angle restraints: No, Simple or Ensemble
> > > dihre = No
> > > dihre-fc = 1000
> > > dihre-tau = 0
> > > ; Output frequency for dihedral values to energy file
> > > nstdihreout = 100
> > >
> > > ; Free energy control stuff
> > > free-energy = no
> > > init-lambda = 0
> > > delta-lambda = 0
> > > sc-alpha = 0
> > > sc-power = 1
> > > sc-sigma = 0.3
> > >
> > > ; Non-equilibrium MD stuff
> > > acc-grps =
> > > accelerate =
> > > freezegrps =
> > > freezedim =
> > > cos-acceleration = 0
> > > deform =
> > >
> > > ; Electric fields
> > > ; Format is number of terms (int) and for all terms an amplitude (real)
> > > ; and a phase angle (real)
> > > E-x =
> > > E-xt =
> > > E-y =
> > > E-yt =
> > > E-z =
> > > E-zt =
> > >
> > > ; User defined thingies
> > > user1-grps =
> > > user2-grps =
> > > userint1 = 0
> > > userint2 = 0
> > > userint3 = 0
> > > userint4 = 0
> > > userreal1 = 0
> > > userreal2 = 0
> > > userreal3 = 0
> > > userreal4 = 0
> > > ___________________________________________________
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> > --
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596, 75124 Uppsala, Sweden
> > phone: 46 18 471 4205 fax: 46 18 511 755
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> >
> > _______________________________________________
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> >
> > ______________________________________________________________________
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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